Hi,
If you have proper termination on outputs you don't need additional circuit protection on inputs.
If you expect significant current spikes or latchup occureance use pullup resistor, serial resistor and external duo diode e.g. BAV-99. This is very good protection for many casses. You can limit input current and input over voltage with value of the serial resistor.
If you need more protection (e.g. noisy enviroment) you can use transil diodes or integrated transil protection arrays.
If you use many inputs from connector to CPLD take care about disipation and overall chip current limits. Also take special care about chip ground to reduce ground bounce and possible floating of input and output voltage levels.
If you route CPLD outputs to connector use serial resistor for proper line termination and output short circuit protection. Also take care overall CPLD current and disipation limits.
If you don't have too many space on the board use only appropriated series SMT RPACKs for input protection.
Don't forget to consider additional signal time propagation produced with input serial resistor and chip input capacitance.